U.K. Maps COVID-19 Spread through Massive Sequencing Project

The U.K. has a plan to sequence and analyze the genetic code of SARS-CoV-2 from as many COVID-19 samples as they can. Scientists, clinicians, academic institutions, and the government have joined together in a massive collaboration to create a map of COVID-19 spread based on whole-genome sequencing.

This effort, named the COVID-19 Genomics UK Consortium (COG-UK) will collect samples from a network of twelve sequencing centers located throughout the U.K., to be sequenced at the Wellcome Trust Sanger Institute in Hinxton, Cambridgeshire. Much of the sequencing performed in the COG-UK program will be supported by Oxford Nanopore Technology. The goal is to deliver large scale, rapid sequencing of the SARS-CoV-2 virus patient samples from confirmed COVID-19 cases and share the results to inform development of drugs, vaccines, and other responses.

“This virus is one of the biggest threats our nation has faced in recent times and crucial to helping us fight it is understanding how it is spreading,” noted Sharon Peacock, PhD, professor of public health and microbiology in the department of medicine at the University of Cambridge and director of the National Infection Service, Public Health England. Harnessing innovative genome technologies, continued Peacock, “will help us tease apart the complex picture of coronavirus spread in the U.K. and rapidly evaluate ways to reduce the impact of this disease on our society.”

Now backed by the National Health Service (NHS) through a £20 million (roughly $23,500,000 U.S. dollars) investment from the government, the consortium will look for breakthroughs that help the U.K. respond to this and future pandemics and save lives.

Nick Loman, PhD, professor of microbial genomics and bioinformatics at the University of Birmingham, tweeted the announcement of COG-UK “after 10 days of rapid setup.”

University of Birmingham’s involvement in the effort brings unique advantages. The university is home to two initiatives—ARTIC and CLIMB—which will play a pivotal role.

The CLIMB project is a cloud-based infrastructure and training for microbial medical bioinformatics that will provide the data analysis pipelines, computing, and storage capacity needed for this large scale project. Featuring over ten petabytes of data storage capacity physically across four sites in the U.K. including Birmingham, CLIMB provides bioinformatics capabilities for the U.K. microbiology community.

The ARTIC Network is a collaborative grant to drive real-time genomic surveillance during outbreaks and epidemics, for real-time viral genome sequencing. Funded by a multi-million dollar Wellcome Trust Collaborative Award to Birmingham, Edinburgh, Cambridge, KU Leuven, the Fred Hutch Center, and UCLA, ARTIC has been involved in major viral outbreaks, notably recently assisting teams in the Democratic Republic of Congo to sequence Ebola. In January, the ARTIC network released a method to sequence SARS-CoV-2 to other researchers globally, built on previous work.

This consortium is focused, noted Loman, “on openness of sequencing and bioinformatics methods, validation, and datasets including rapid deposition.” The data will be shared with the GISAID, a global initiative on sharing avian flu data that was started in 2008 as a mechanism for the rapid sharing of influenza data. The data will also be shared with the European Nucleotide Archive (ENA) which offers open data archiving across species, platforms, and applications. This openness and collaboration, noted Loman, will “further our understanding of epidemiology/biology but also to help other countries in rapid set-up phase.”